3iqe: Difference between revisions
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<StructureSection load='3iqe' size='340' side='right'caption='[[3iqe]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='3iqe' size='340' side='right'caption='[[3iqe]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3iqe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3iqe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IQE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IQE FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=F42:COENZYME+F420'>F42</scene>, <scene name='pdbligand=H4M:5,10-DIMETHYLENE+TETRAHYDROMETHANOPTERIN'>H4M</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=F42:COENZYME+F420'>F42</scene>, <scene name='pdbligand=H4M:5,10-DIMETHYLENE+TETRAHYDROMETHANOPTERIN'>H4M</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3iqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iqe OCA], [https://pdbe.org/3iqe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iqe RCSB], [https://www.ebi.ac.uk/pdbsum/3iqe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iqe ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3iqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iqe OCA], [https://pdbe.org/3iqe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iqe RCSB], [https://www.ebi.ac.uk/pdbsum/3iqe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iqe ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/MTD_METKA MTD_METKA] Catalyzes the reversible reduction of methenyl-H(4)MPT(+) to methylene-H(4)MPT.<ref>PMID:9151968</ref> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Methanopyrus kandleri]] | ||
[[Category: Ceh | [[Category: Ceh KE]] | ||
[[Category: Demmer | [[Category: Demmer U]] | ||
[[Category: Ermler | [[Category: Ermler U]] | ||
[[Category: Moll | [[Category: Moll J]] | ||
[[Category: Shima | [[Category: Shima S]] | ||
[[Category: Thauer | [[Category: Thauer RK]] | ||
[[Category: Warkentin | [[Category: Warkentin E]] | ||
Latest revision as of 19:02, 1 November 2023
Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin and coenzyme F420Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin and coenzyme F420
Structural highlights
FunctionMTD_METKA Catalyzes the reversible reduction of methenyl-H(4)MPT(+) to methylene-H(4)MPT.[1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedF(420)-dependent methylenetetrahydromethanopterin (methylene-H(4)MPT) dehydrogenase (Mtd) of Methanopyrus kandleri is an enzyme of the methanogenic energy metabolism that catalyzes the reversible hydride transfer between methenyl-H(4)MPT(+) and methylene-H(4)MPT using coenzyme F(420) as hydride carrier. We determined the structures of the Mtd-methylene-H(4)MPT, Mtd-methenyl-H(4)MPT(+), and the Mtd-methenyl-H(4)MPT(+)-F(420)H(2) complexes at 2.1, 2.0, and 1.8 A resolution, respectively. The pterin-imidazolidine-phenyl ring system is present in a new extended but not planar conformation which is virtually identical in methenyl-H(4)MPT(+) and methylene-H(4)MPT at the current resolution. Both substrates methenyl-H(4)MPT(+) and F(420)H(2) bind in a face to face arrangement to an active site cleft, thereby ensuring a direct hydride transfer between their C14a and C5 atoms, respectively. The polypeptide scaffold does not reveal any significant conformational change upon binding of the bulky substrates but in turn changes the conformations of the substrate rings either to avoid clashes between certain ring atoms or to adjust the rings involved in hydride transfer for providing an optimal catalytic efficiency. Structural Basis of the Hydride Transfer Mechanism in F(420)-Dependent Methylenetetrahydromethanopterin Dehydrogenase.,Ceh K, Demmer U, Warkentin E, Moll J, Thauer RK, Shima S, Ermler U Biochemistry. 2009 Sep 29. PMID:19761261[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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